Just the two of us
by Chosenshadowhunter
Summary: Jonathan goes to New York to find his sister and learns she doesn't know that she is a shadowhunter. Using the name Sebastian he befriends her and opens up a new world for her. When she meets Jace, Sebastian couldn't be more enraged to see his father's other son. He does everything he can to have to her to himself even if that means removing Jace from her life. M for future Lemons.
1. Chapter 1

_I have a sister and I will teach her to love me. My name is **Jonathan**, but everyone calls me **Sebastian **and I am going to burn down the world._

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><p>His sword felt light as he swung it around in his hand, the metal was warm beneath his fingertips. He darted forward sending the tip of his blade directly into the demon's heart, he jumped backwards as it exploded into the air and ichor flew everywhere. Quickley he spun around on his feet and charged at the second on coming demon and sliced his word through it's neck, decapitating it. He smiled whilst placing his weapon into it's sheath, not bothering to wipe the demon blood off.<p>

"How was that father?" He said, awaiting approval. When he glanced up Valentine was standing with his back against the brick wall that surrounded the alley way. He was wearing his gear and his hood covered his face. Jonathan could tell there was no hint of a smile playing on his features and sighed under his breath.

"You can do better, We will train until you cannot train any longer understand?." His fathers voice was quite and the least bit threatening but Jonathan obeyed regardless. He was sick of demon hunting and bending at his fathers will but he had promised him his family. He wasn't entertained at the idea of having his mother back after all, she had abandoned him when he was a small child, she deserved to be left alone, with no family. His sister on the other hand was the reason he was doing all of this. His father had spoke of her in such disgust, blaming her for Jocelyn leaving him but it wasn't her fault. Jonathan found himself picturing what she would look like, his father had told him all about his mother so he assumed she would look like her. Red hair like fire and green eyes like the grass.

The night was long and full of blood shed as Jonathan sliced his way through a good amount of demons, he found it boring it was too easy for him. Since he could remember he had never found a worthy opponent, every creature he faced was everything but a challenge. There was one person he wanted to fight with face to face, and that was the other Jonathan. Father's angel boy. One child angel the other a demon. father's plan hadn't worked out the way he had planned many years ago. One child was too soft and weak. The other was too cruel, sadistic and uncontrollable. Jonathan smiled to himself, he had been the better offspring, the most powerful in all aspects.

That night he found himself unable to sleep, he twisted and turned in annoyance until finally he got out of his bed. He got himself dressed and started packing a bag, he slung it over his shoulder after he closed it.

He didn't bother telling his father directly that he was leaving, instead left him a blunt note. " Father, I'm going to New York. I have to find her. - Jonathan." He scribbled the words quickly and walked through into the kitchen. He dropped the note onto the counter and then with his stele he traced the rune onto the grey wall and stepped through it once he was done.

In a matter of minutes he found himself walking through the busy streets of New York, He knew he would have to do some research find out exactly where she was. He stayed at a hotel which gave him usage to a computer and started typing. It was a long process considering he didn't have a clue what her second name was. He eventually found himself on a website, Facebook. He went through every Clarissa situated in New york until he found her. She was more beautiful than he had ever imagined. He looked at her pictures for a while before he noticed she was going to a mundane club. Pandemonium. He grinned this would be his chance, he could meet her tonight.

He didn't bother with mundane transport and portaled himself to the night club. He stood across the street staring over at it. He wondered if his sister knew she was a shadowhunter and then he paused. He knew he couldn't tell her his real name he was aware their mother might have told her about him. His mind raced until he remembered the Verlac family, their son was about his age, right height and looked similar. The only difference was the hair colour and he was not going to dye his platinum blonde hair black, it would be too much of an annoyance.

He strode forward his large black boots thudded against the road beneath him. As he got closer he could see the runes that covered the buildings walls and almost rolled his eyes. Of course his sister would be in a Shadowhunter attraction. He would have to be careful, his father wasn't very welcome amongst the Nephilim and he knew the same would go for him. He didn't bother waiting in line with other mundanes and walked straight in. No one stopped him and he assumed it was because of the black markings that covered his skin.

The inside of the club was layered with smoke and various colours of light flashed around amongst the dancers, that were in the center of the room. His eyes scanned the crowd but to his disappointment he couldn't see her. He decided to get himself a drink and headed towards the bar. He could feel the stares on him as girls around him giggled looking at him shyly. He knew he was attractive and it gave him an advantage in the mundane world. Not many people said no to a pretty face.

"Hi!" A girl went out her way to stand in front of him and he glanced down at her small frame, long blonde hair framed her heart shaped face and her blue eyes were gaping up at him. She was not his type, his type was a red haired, green eyes beauty. He knew he couldn't just push her out of his way like he would have done if it were any other situation, he would draw too much attention to him. "Go away, I'm not interested." He spoke quietly but she heard him, her eyes widened in shock at being rejected. She would have been beautiful to him if he hadn't already laid eyes on Clarissa but now she was all he could see in his mind. The girl stepped aside and walked over to her surprised giggling friends.

When he reached the bar he turned his back to it and looked across the dancefloor and then he saw the vibrant red hair illuminated by the strobe lights. She wasn't alone and he frowned, he had been hoping she would be. He pushed himself forward in her direction and strode past the dancers, their clumsy elbows didn't bother him as they jabbed at his sides. He was next to her now and he almost sighed, she was perfection. He wanted her to be his and she will be he reminded himself. She was moving her body the same way as the people around her were but she looked more graceful. He noticed her arms were bare, free of any runes. He was about to speak when her eyes were looking into his and she smiled at him. He felt himself return the smile and held out his hand to her.

"Hello, I'm Sebastian. I was wondering, Would you like to dance?" He spoke slowly so she could make him out over the music and when she reached out and grabbed his hand his heart felt like it stopped. Her small hand fit perfectly in his and he clasped his fingers around her palm and his arm wrapped around her waist, pulling her to him. He couldn't believe that after waiting sixteen years she was now in front of him and they were dancing together and then he knew that no matter what it would not be the last time.

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><p>Please review, I'm not sure if I am going to carry on with this story.<p> 


	2. Chapter 2

His hopes of having a conversation with her were short lived when a tall thin boy walked over to them and Clary released Jonathan from her grasp.

"Simon.." She grinned at him and he frowned was this her boyfriend, he felt a strong urge to punch the brown haired boy clean in the face and smash his glasses that sat on the bridge of his nose. "This is Sebastian" She continued and he focused his gaze on her as she spoke, choosing to completely ignore the skinny boy in front of him. "Yeah, hey." Simon said dismissively and Jonathan could feel the boys eyes on him.

For some reason this kid really annoyed him and when he eventually dragged his gaze away from his sister to look at the scrawny mundane he was staring at Clarissa in a way he didn't like, in a way only he should look at her. He pushed his hands into his jean pockets and dug his fingers into his thighs. He felt pathetic for feeling so jealous, He wasn't naive he knew it wouldn't be normal if he started shouting at this boy to go away but every fibre in his body was telling him to do it anyway, he kept silent and bit his tongue.

"We should really be heading home now." Simon said pushing his glasses up with one finger, he was staring at Jonathan from the corners of his eyes. Jonathan couldn't let her leave now not when they just met. "That's a shame I was going to ask if you wanted to go for a coffee, I would make sure you got home safe." He offered and watched as she fixed her large green eyes on his own, her lips tugged up into beautiful smile and she took a step towards him and gave Simon an apologetic smile. "Actually I'm going to go for some Coffee, Si. Why don't you come?" She shrugged gently. Jonathan willed for him to say no.

"Nah, I'm good. Don't wanna be third wheeling on your first date." He said and waved goodbye to her while turning around and walking away. Clarissa called out correcting him about it not being a date but he had disappeared amongst the crowd. Good riddance Jonathan thought to himself feeling slightly smug.

"So, Coffee then?" Her voice was like music to his ears and he nodded, grabbing her hand. He escorted her out of the club and the cold air against his skin was a relief, it had been far to hot for him in there and it had left his skin feeling sticky, he tried not to think about it.

He looked down at her an with apologetic smile. " I don't know my way around here, The whole going for coffee thing was just a ruse, truth be told I'm just in dire need of a free tour guide." His grin was wide and he laughed when he caught the sight of her expression. "I'm only kidding, I do want to go for coffee, as well." This time she laughed and smiled up at him.

"You know what? I will give you a free tour if you buy the coffee." She said in between laughs. He was glad she had some sort of humour about her, if she had been boring that would have been a disappointment. He followed Clary and cursed mentally at his slip up. " So, whats your name?" He asked her. If he wanted to blend in he really had to start acting like he didn't know everything, it was to early for her to know who he really was.

"It's Clary." She said casually and then it sunk in how close he could have came to blowing his whole plan into tiny unfixable pieces. He would have called her Clarissa and then if she asked him how he knew her name he wouldn't have been able to save himself by saying he overheard her friend using it.

They were only walking for a short period of time before she stopped abruptly in front of a small coffee shop that appeared to be open all night, when they walked in only a few people were sat the booths that ran along the windows. He told Clary to go get them a table and he went to the counter and ordered them both coffee. He didn't drink the stuff normally, he thought it tasted revolting and couldn't understand why anyone would want to drink it willingly.

He regretted not asking her if she wanted to go for a walk or to go get something to eat. He carried the two mugs to the far back of the cafe and placed hers down onto the table in front of her. "Thanks" She murmured and took a sip he figured he should do the same so he took a drink from his own mug and forced it down his throat and tried to prevent himself from gagging at the taste.

"Where are you from then? you have an accent." She pointed out and luckily Jonathan had rehearsed what he would tell her earlier that night. "I'm from England, I only moved here a few days ago. I live with my father but he is busy, his work takes him away often." Speaking of his father made him wonder if he was looking for him. He assumed he would be since he was on a mission to find to the mortal cup which Jocelyn had stolen when she left him but Jonathan had no real interest in his fathers plan. All he wanted was to be with Clary and here she was sitting in front of him, so nothing else mattered to him.

" I have always lived in Brooklyn." She sighed. " I would love to see another country." He gave her a warm smile and raised his mug to his lips, pretending to have a drink. "You would love England. It's beautiful" He said grinning down at her. "Hopefully one day you will get to visit Somewhere." She smiled at him. He would take her one day, show her the world, soon he thought.

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><p>Clary had told him her house wasn't far away and she could get a cab home but he told her to keep her money and that he would walk her home. She had agreed almost immediately and he hoped he was having an effect on her. She didn't seem phased by his looks like most other girls who when they spoke to him suddenly became stupid - if it was an act he couldn't tell- and started acting ridiculous.<p>

He grinned remembering when one time a while back a girl presented herself to him offering all sorts, but had made it obvious she probably couldn't spell her own name. " If I wanted to have sex with someone withought an IQ, I would buy a sexdoll." He had said to her and she had started crying right in front of him, he wasn't sure how to respond so had laughed at her. He knew now that the slap he had gotten was truly earned.

Though he liked that about Clary it made it hard for him to tell if she found him attractive and it was starting to annoy him. As they walked he listened to her with interest as she told him about her life, how she liked to draw, her best friend Simon even though he vaguely payed attention to that part and she told him about their mother. Before he knew it they had stopped outside her house. He grinned down at her. "Well it was nice meeting you, I would like to go out again sometime?" He said as his gaze fixed on her small face. Then for the first time that night he saw her cheeks turn red.

"I would love to. why don't we meet tomorrow at the coffee shop?" She offered and pulled her jacket tighter around her body, emphasizing her curves in all the right places. He had almost forgetten the question when he finally replied. "That sounds great." They fell silent but it wasn't uncomfortable then Jonathan reached his hand out and cupped her face brushing her cheek with his thumb lightly, the skin underneath was soft against his own.

He leaned forwards and put his lips against hers gently. When she responded to him electricity ran through his veins and he pulled her to him more urgently and the kiss deepened. He felt her tongue as her lips opened allowing him in, the warmth of her sent shivers through him and then she pulled away breathing harshly and he didn't realise he was doing the same.

"I should go inside now." Her voice broke the silence but Jonathan barley made her out as the blood pounded in his ears but he nodded. "I will see you tomorrow, Clary." He said quietly and he loved the way her name rolled off his tongue. He watched her as she climbed up the stairs to her front door then disappeared inside. He stood there for another minute or so until he had gotten his breath back then headed for his hotel.

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><p><strong><em>Thanks for reading, Please leave a review if you can and let me know if you enjoying ithating it. All feedback is welcome._**


	3. Chapter 3

Slowly he opened his eyes with a yawn escaping his lips. The sun shined through the window colouring the room with golden rays which stung at his eyes. He sat up and stretched feeling the familiar tightness that rippled through his back, bringing the memories of Valentine whipping him as a child fresh in to his mind. His father had said it was a lesson about the price of obedience, but he knew better. His father trained him to be a soldier, to be a weapon. Jonathan knew the whipping was a way to give Valentine a form of control.

He rose to his feet and glanced at the clock that hung loosely on the wall. It was almost eleven. He realised that him and Clary hadn't arranged a time to meet, so quickley he pulled on his clothes and made his way outside. He hailed a cab and told the driver the name of the coffee shop, Java Jones. Jonathan decided we would wait for her there, even if it took all day. Twenty minutes later he was stood outside the small shop, he went inside and ordered himself a water and sat down beside the window.

He was on his fourth bottle when he sensed someone standing at the table. His eyes shot up expecting to see his sister. Valentine was wearing his black gear and as far as Jonathan could tell he didn't look amused as he took a seat opposite him. He was about to open his mouth to speak when his fathers words filled the silence. " Why do you defy me?." His eyes levelled with his own, Valentine's eyebrows were pulled together as he frowned.

" I could lie and say I don't choose too, but well that would be lying." He felt his lips turn up into a smirk. He was in no mood to have this discussion with him, but he knew his father wouldn't drop it. He saw his face turn red with anger and he almost wanted to laugh. "Get home now Jonathan, you shouldn't be here. I have put myself at risk coming to get you." His expression was stern and Jonathan pretended to consider him for a moment. "Nah, I like it here actually." He said. "I'm making mundie friends." His grin widened as he watched the veins in his fathers forehead pulse. "You can't make me come with you, you have no control over me." He continued and watched the realisation come clear in Valentines eyes then he abruptly stood up.

"Fine Jonathan but remember there are multiple ways of control." He turned around and walked out of the shop. Jonathan would have considered his threat but it didn't phase him, he could handle his father. He had been taught well. His thoughts turned back to Clarissa and he started wondering where she was, it was getting late. He started to panic, what if she didn't like him. Was he to forward with the kiss they shared? His mind raced then he found himself outside walking to her house.

It was still light outside but the sun was hidden behind the tall buildings around him, soon enough he was standing in front of her small house. His eyes widened in shock as he saw the door hanging by one hinge and without thinking he ran inside. It was dark the only light that entered the house was from outside. The furniture was scattered along the floor and he felt a lump rise in his throat. As he entered the kitchen he saw a small body shied away in the corner and he blew out the breath that he didn't know he was holding, Clarissa.

He walked towards her slowly in an attempt not to frighten her. Her head turned up to look at him and her wide eyes were red and puffy. He found himself just wanting to hold her and comfort her, the feelings overwhelmed him. "Clary?" His voice was soft and he knelt down beside her offering her his hand. She took it and he pulled her up on to her feet, she was shaking and he wrapped his arms around her shoulders. "What happened here?" He said and he had a horrible feeling that it was their father.

"Two men came" Her voice sounded so fragile, like she could be broken so easily. "They took my mother, sebastian." She continued and then he knew it had been Valentine but what he didn't understand was why take something he had no desire for, then he looked down at the distraught girl in his arms and unexplainable anger surged through him, seeing her like this was their father's doing and instantly he understood Valentines actions. "We will get her back Clary, I promise" He whispered down at her and she surprised him when she pulled out of his reach. The expression on her features wasn't hurt it was anger.

"You don't know that!" She shouted at him. " This has nothing to do with you." She was sobbing as she spoke and seeing her tugged at his heart, he had never experience this kind of pain before, he didn't like it. He knew he would have to explain to her what she was, what he was regardless of how bad the timing was. "Clary listen to me!" He interrupted her and she stared him blankly. "We need to talk, it's important" He spoke slowly and as she was about to start ranting again he took a deep breath. "I think I know who took your mother" He said it carefully and then her eyes widened with surprise then she looked at him suspiciously.

He ignored her stare and grabbed her hand and led her to the living room. He pulled up one of the chairs from the floor and set it down gesturing for her to sit. She did and he knelt down in front of her placing his hands on her thighs. "Have you heard about stories of angels and demons?" He paused and looked at her and when she nodded he carried on. "Well... all the stories are true." He was interrupted as she laughed at him hysterically. He ignored it and proceeded to tell her what she needed to know. " You are half-angel Clarissa Morgenstern." Her laughter stopped at the use of her name and she shook her head. "My last name is Fray, not Morgenstern." She said bewildered.

A sigh escaped his lips, he had been hoping this would have been easy. "No it's not. You have to listen to me carefully, okay? You are a shadowhunter, I am one too." He willed for her too remember but she was staring at him like he was crazy. He needed a warlock. "You need to trust me" His eyes bored into hers and she looked skeptical for a moment but she nodded. He took her hand and pulled her up out of the chair and took her outside. He waved down a cab and they both got inside he gave the driver the address. Sighing he relaxed himself against the leather.

Jonathan knew what he was doing was the quickest way for Clary too realise what she is but it didn't mean he had to like it. They were in for a long night and from what Jonathan had heard Magnus Bane was quite the party animal.

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><p>Sorry for the rushed chapter, I wrote this on my phone as I don't always have access to a computer. Please remember to review!<p> 


	4. Chapter 4

They could only go so far by car until they had to walk, wards were all around the warlocks home to keep mundanes away. Jonathan walked ahead of Clary as they made there way up the path to the large gold front door. He knocked three times then dropped his hand and it hung loosely at his side. He was aware that most warlocks done favours and such for money but he was more than willing to use brute force, after all it was in his nature. He had been on his best behaviour for too long and the demon part of him was scratching at the surface.

The door flung open wide and a small man - probably a servant Jonathan thought- stood wearing black clothing. He had bright purple hair and dark brown pupils covered most of his eyes. "What can I do for you?" He spoke politely but he looked at them suspiciously. Jonathan didn't know why until he realised it was because they were shadowhunters, his bare arms were covered in black runes, some old, some new. " We have come to see Magnus Bane. We require his assistance." He glared at the small man as he waited for him to speak. The dull beat of music flowed from the room behind him. The man's eyes narrowed then quickly told them no, he started to close the door on them but Jonathan shot out his hand, stopping it from shutting.

"I don't think you understood me, I have came to see Magnus, regardless of whether he wants to see me or not." His voice was low and husky and he felt the smirk spread across his face as he watched the man flinch away from him. Jonathan gestured for Clary to go through the door and when she hesitated he grabbed her hand and pulled her inside. They walked through the second door and entered a large open room. It was filled with partying downworlders. He stared down at Clary. " Stay beside me and don't eat or drink anything, okay?"He said whispering in her ear and when she nodded he continued walking towards the center of the room.

Eyes were on them both as they made their way past the downworlders, he stopped near a female vampire. She looked at him like he was dirt but he ignored it. "Where is Magnus Bane?" He spoke quietly and was glad when the vampire showed him with no questions asked. With Clary close behind him he made his way over to the door in the far corner and when they got close it flew open. A tall blue haired man walked out. Jonathan gave him a well rehearsed smile but it wasn't returned, the warlock was wasn't even looking in his direction instead his gaze was fixed on his sister.

"Clarissa?" The man said, his cat-like eyes that were surrounded with glitter were wide with surprise. "What are you doing here?". Jonathan watched her as she shrugged her shoulders, just as baffled as he was. "How do you know her, warlock?" Jonathans tone was cold as he spoke and he pointed to the small room that Magnus had just came out of. "We will speak in there." Magnus' yellow eyes narrowed but he complied and stalked back through the door.

Clary was the first one to speak as the door closed behind them. "How do you know my name? You act as though you know me?." She spoke so fast her words came out jumbled but from the look Magnus gave her it showed he understood. "I know your mother, I have since you were a child. You have met me a few times." He looked uneasy like he didn't want to be there, having this conversation. The room fell silent and as Jonathan was about to speak Clary bet him to it. " I don't remember ever meeting you, I think you are mistaken." Her words hung in the air and Magnus looked like he was trying to find the right words to say.

"Clarissa as you know I am a warlock..." Her expression showed she didn't and his yellow eyes looked over at Jonathan and narrowed as if he were mentally scolding him then he carried on. " Your mother has been bringing you to me every year for sixteen years, she couldn't afford to pay for my services but I helped her regardless. All I had to do was remove your memories of the shadow world." He stopped, letting her process what he was telling her. Her face was composed and she was nodding slowly, Jonathan tried not to think about how pale her skin was turning.

"Sorry to interrupt your extremely boring story telling but it's time to give her back her memories. We need to be going, her mother was kidnapped." Jonathan had never been a patient person and he was becoming bored, he wanted what they came for so they could leave but as he watched Magnus' face drop he sighed, annoyed. " Uhg... al wait outside. Do what you can Warlock." he waved at him dismissively and walked over to Clary. He pressed his lips to her forehead and took a deep breath. " I will just be outside, come and get me if you need me." He spoke softly. " Okay" She mumbled against his chest then he pulled away from her and walked out the room.

He stood on the other side of the door like he had promised Clary and he watched as a group of warlocks shot blue sparks from their fingertips at each for entertainment, their laughter filled the room. He pictured himself with a sword making his way around the room, slaughtering them all one by one. It brought a smile to his lips. It felt like days, weeks since he last killed anything and he missed the blood shed. The adrenaline of watching your opponent take his last breath, their body struggeling for air as they bled out. A shiver ran through his spine, he considered what the outcome would be if he just dragged one of the downworlders outside and fought it but he knew it would mean scaring his sister away. He pushed the thoughts aside and concentrated on her instead.

It wasn't long before Clary emerged from the room looking confused. "That was just weird." She said and looked up at him and looked startled. " When did you get tattoo's?" She stared at him bewildered. Magnus appeared behind her and he was looking at Jonathan. " All I could do was help her to see past the glamour, she would have been due to see me in a few days anyway, the memories will come back to her but that's all I can do now." He shrugged and continued. " I suggest you go to the New York Institute, Shadow hunter. The more of your own kind she's around the better, It might help to jog her memory, here is the address if you don't already know it" He said and grabbed a piece of paper, scribbling down the words quickly and handed it to Jonathan, his eyebrows pulled together as he frowned. "And please don't come back, there is nothing else I can do to help and my guest's get nervous around the Nephilim, as you can imagine." Jonathan didn't take any offence at the warlocks words, he considered it a compliment there was nothing wrong with being feared, it was power.

They were outside now and Clary looked so tired it that it made Jonathan want to cuddle her until she fell asleep in his arms. He remembered Magnus' advice about the New york Institute and instantly wished he was able to track his father. Valentine was smart and he wouldn't make himself easily found, this was punishment for disobeying him. He would have known physically harming him wouldn't work, Jonathan would kill him before he had a chance to lay a finger on him, or another whip. Valentine was already controlling him now and it angered him, he had never been subject to feelings, and his father was taking full advantage of it.

"Are we going to this Institute then?" Clary's voice broke the silence and he stared down at her small face. Her eyes were large as they settled on his, he let out a sigh and placed his hand in hers. "Yes, I suppose we are." He said gently and then they started walking towards the main road at the end of the street.

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><p><strong>Thank's for all of your reviews. Hope you enjoyed this chapter. Next update will be soon.<strong>


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